Flye

Introduction

Flye: Fast and accurate de novo assembler for single molecule sequencing reads.

For more information, please check its website: https://biocontainers.pro/tools/flye and its home page on Github.

Versions

• 2.9.1

• 2.9.2

• 2.9

Commands

• flye

Module

You can load the modules by:

module load biocontainers
module load flye

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Flye on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=flye
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers flye

flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --threads 12
flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --threads 12